Impact on Patients' Treatment Outcomes of XpertMTB/RIF Implementation for the Diagnosis of Tuberculosis: Follow-Up of a Stepped-Wedge Randomized Clinical Trial

Factors associated with tuberculosis treatment initiation among bacteriologically negative individuals evaluated for tuberculosis: an individual patient data meta-analysis

Background

Globally, over one-third of pulmonary tuberculosis (TB) disease diagnoses are made based on clinical criteria after a negative diagnostic test result. Understanding factors associated with clinicians' decisions to initiate treatment for individuals with negative test results is critical for predicting the potential impact of new diagnostics.

Methods

We performed a systematic review and individual patient data meta-analysis using studies conducted between January/2010 and December/2022 (PROSPERO: CRD42022287613). We included trials or cohort studies that enrolled individuals evaluated for TB in routine settings. In these studies participants were evaluated based on clinical examination and routinely-used diagnostics, and were followed for ≥1 week after the initial test result. We used hierarchical Bayesian logistic regression to identify factors associated with treatment initiation following a negative result on an initial bacteriological test (e.g., sputum smear microscopy, Xpert MTB/RIF).

Findings

Multiple factors were positively associated with treatment initiation: male sex [adjusted Odds Ratio (aOR) 1.61 (1.31-1.95)], history of prior TB [aOR 1.36 (1.06-1.73)], reported cough [aOR 4.62 (3.42-6.27)], reported night sweats [aOR 1.50 (1.21-1.90)], and having HIV infection but not on ART [aOR 1.68 (1.23-2.32)]. Treatment initiation was substantially less likely for individuals testing negative with Xpert [aOR 0.77 (0.62-0.96)] compared to smear microscopy and declined in more recent years.

Interpretation

Multiple factors influenced decisions to initiate TB treatment despite negative test results. Clinicians were substantially less likely to treat in the absence of a positive test result when using more sensitive, PCR-based diagnostics.

Assessing exposure-time treatment effect heterogeneity in stepped-wedge cluster randomized trials

A stepped-wedge cluster randomized trial (CRT) is a unidirectional crossover study in which timings of treatment initiation for clusters are randomized. Because the timing of treatment initiation is different for each cluster, an emerging question is whether the treatment effect depends on the exposure time, namely, the time duration since the initiation of treatment. Existing approaches for assessing exposure-time treatment effect heterogeneity either assume a parametric functional form of exposure time or model the exposure time as a categorical variable, in which case the number of parameters increases with the number of exposure-time periods, leading to a potential loss in efficiency. In this article, we propose a new model formulation for assessing treatment effect heterogeneity over exposure time. Rather than a categorical term for each level of exposure time, the proposed model includes a random effect to represent varying treatment effects by exposure time. This allows for pooling information across exposure-time periods and may result in more precise average and exposure-time-specific treatment effect estimates. In addition, we develop an accompanying permutation test for the variance component of the heterogeneous treatment effect parameters. We conduct simulation studies to compare the proposed model and permutation test to alternative methods to elucidate their finite-sample operating characteristics, and to generate practical guidance on model choices for assessing exposure-time treatment effect heterogeneity in stepped-wedge CRTs.

Cost-effectiveness of GeneXpert Omni compared with GeneXpert MTB/Rif for point-of-care diagnosis of tuberculosis in a low-resource, high-burden setting in Eastern Uganda: a cost-effectiveness analysis based on decision analytical modelling

OBJECTIVE

To determine the cost-effectiveness of Xpert Omni compared with Xpert MTB/Rif for point-of-care diagnosis of tuberculosis among presumptive cases in a low-resource, high burden facility.

DESIGN

Cost-effectiveness analysis from the provider's perspective.

SETTING

A low-resource, high tuberculosis burden district in Eastern Uganda.

PARTICIPANTS

A provider's perspective was used, and thus, data were collected from experts in the field of tuberculosis diagnosis purposively selected at the local, subnational and national levels.

METHODS

A decision analysis model was contracted from TreeAge comparing Xpert MTB/Rif and Xpert Omni. Cost estimation was done using the ingredients' approach. One-way deterministic sensitivity analyses were performed to identify the most influential model parameters.

OUTCOME MEASURE

The outcome measure was incremental cost per additional test diagnosed expressed as the incremental cost-effectiveness ratio.

RESULTS

The total cost per test for Xpert MTB/Rif was US$14.933. Cartridge and reagent kits contributed to 67% of Xpert MTB/Rif costs. Sample transport costs increased the cost per test of Xpert MTB/Rif by $1.28. The total cost per test for Xpert Omni was $16.153. Cartridge and reagent kits contributed to over 71.2% of Xpert Omni's cost per test. The incremental cost-effectiveness ratio for using Xpert Omni as a replacement for Xpert MTB/Rif was US$30.73 per additional case detected. There was no dominance noted in the cost-effectiveness analysis, meaning no strategy was dominant over the other.

CONCLUSION

The use of Xpert Omni at the point-of-care health facility was more effective but with an increased cost compared with Xpert MTB/Rif at the centralised referral testing facility.

Impact of diagnostic strategies for tuberculosis using lateral flow urine lipoarabinomannan assay in people living with HIV

BACKGROUND

Tuberculosis is the primary cause of hospital admission in people living with HIV, and the likelihood of death in the hospital is unacceptably high. The Alere Determine TB LAM Ag test (AlereLAM) is a point-of-care test and the only lateral flow lipoarabinomannan assay (LF-LAM) assay currently commercially available and recommended by the World Health Organization (WHO). A 2019 Cochrane Review summarised the diagnostic accuracy of LF-LAM for tuberculosis in people living with HIV. This systematic review assesses the impact of the use of LF-LAM (AlereLAM) on mortality and other patient-important outcomes.

OBJECTIVES

To assess the impact of the use of LF-LAM (AlereLAM) on mortality in adults living with HIV in inpatient and outpatient settings. To assess the impact of the use of LF-LAM (AlereLAM) on other patient-important outcomes in adults living with HIV, including time to diagnosis of tuberculosis, and time to initiation of tuberculosis treatment.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register; the Cochrane Central Register of Controlled Trials (CENTRAL); MEDLINE (PubMed); Embase (Ovid); Science Citation Index Expanded (Web of Science), BIOSIS Previews, Scopus, LILACS; ProQuest Dissertations and Theses; ClinicalTrials.gov; and the WHO ICTRP up to 12 March 2021.

SELECTION CRITERIA

Randomized controlled trials that compared a diagnostic intervention including LF-LAM with diagnostic strategies that used smear microscopy, mycobacterial culture, a nucleic acid amplification test such as Xpert MTB/RIF, or a combination of these tests. We included adults (≥ 15 years) living with HIV.

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed trials for eligibility, extracted data, and analysed risk of bias using the Cochrane tool for assessing risk of bias in randomized studies. We contacted study authors for clarification as needed. We used risk ratio (RR) with 95% confidence intervals (CI). We used a fixed-effect model except in the presence of clinical or statistical heterogeneity, in which case we used a random-effects model. We assessed the certainty of the evidence using GRADE.

MAIN RESULTS

We included three trials, two in inpatient settings and one in outpatient settings. All trials were conducted in sub-Saharan Africa and assessed the impact of diagnostic strategies that included LF-LAM on mortality when the test was used in conjunction with other tuberculosis diagnostic tests or clinical assessment for clinical decision-making in adults living with HIV. Inpatient settings  In inpatient settings, the use of LF-LAM testing as part of a tuberculosis diagnostic strategy likely reduces mortality in people living with HIV at eight weeks compared to routine tuberculosis diagnostic testing without LF-LAM (pooled RR 0.85, 95% CI 0.76 to 0.94; 5102 participants, 2 trials; moderate-certainty evidence). That is, people living with HIV who received LF-LAM had 15% lower risk of mortality. The absolute effect was 34 fewer deaths per 1000 (from 14 fewer to 55 fewer). In inpatient settings, the use of LF-LAM testing as part of a tuberculosis diagnostic strategy probably results in a slight increase in the proportion of people living with HIV who were started on tuberculosis treatment compared to routine tuberculosis diagnostic testing without LF-LAM (pooled RR 1.26, 95% CI 0.94 to 1.69; 5102 participants, 2 trials; moderate-certainty evidence).  Outpatient settings In outpatient settings, the use of LF-LAM testing as part of a tuberculosis diagnostic strategy may reduce mortality in people living with HIV at six months compared to routine tuberculosis diagnostic testing without LF-LAM (RR 0.89, 95% CI 0.71 to 1.11; 2972 participants, 1 trial; low-certainty evidence). Although this trial did not detect a difference in mortality, the direction of effect was towards a mortality reduction, and the effect size was similar to that in inpatient settings.  In outpatient settings, the use of LF-LAM testing as part of a tuberculosis diagnostic strategy may result in a large increase in the proportion of people living with HIV who were started on tuberculosis treatment compared to routine tuberculosis diagnostic testing without LF-LAM (RR 5.44, 95% CI 4.70 to 6.29, 3022 participants, 1 trial; low-certainty evidence). Other patient-important outcomes Assessment of other patient-important and implementation outcomes in the trials varied. The included trials demonstrated that a higher proportion of people living with HIV were able to produce urine compared to sputum for tuberculosis diagnostic testing; a higher proportion of people living with HIV were diagnosed with tuberculosis in the group that received LF-LAM; and the incremental diagnostic yield was higher for LF-LAM than for urine or sputum Xpert MTB/RIF.

AUTHORS' CONCLUSIONS

In inpatient settings, the use of LF-LAM as part of a tuberculosis diagnostic testing strategy likely reduces mortality and probably results in a slight increase in tuberculosis treatment initiation in people living with HIV. The reduction in mortality may be due to earlier diagnosis, which facilitates prompt treatment initiation. In outpatient settings, the use of LF-LAM testing as part of a tuberculosis diagnostic strategy may reduce mortality and may result in a large increase in tuberculosis treatment initiation in people living with HIV. Our results support the implementation of LF-LAM to be used in conjunction with other WHO-recommended tuberculosis diagnostic tests to assist in the rapid diagnosis of tuberculosis in people living with HIV.

Mortality and associated factors among adult patients on tuberculosis treatment in Tanzania: A retrospective cohort study

INTRODUCTION

Tuberculosis (TB) is the global leading cause of death from an infectious agent. Tanzania is among the 30 high TB burden countries with a mortality rate of 47 per 100,000 population and a case fatality of 4%. This study assessed mortality rate, survival probabilities, and factors associated with death among adult TB patients on TB treatment in Tanzania.

METHODS

A retrospective cohort study was conducted utilizing case-based national TB program data of adult (≥15 years) TB cases enrolled on TB treatment from January 2017 to December 2017. We determined survival probabilities using the Kaplan-Meier estimator and a Cox proportional hazard model was used to identify independent risk factors of TB mortality. Hazard ratios and their respective 95% confidence intervals were reported.

RESULTS

Of 53,753 adult TB patients, 1927 (3.6%) died during TB treatment and the crude mortality rate was 6.31 per 1000 person-months. Male accounted for 33,297 (61.9%) of the study population and the median (interquartile range [IQR]) age was 40 (30-53) years. More than half 1027 (56.7%) of deaths occurred in first two months of treatment. Overall survival probabilities were 96%, and 92% at 6th and 12th month respectively. The independent risk factors for TB mortality among TB patients included: advanced age ≥ 45 years (adjusted hazard ratio (aHR) = 1.74, 95% confidence interval (CI) = 1.45-2.08); receiving service at the hospital level (aHR = 1.22, 95% CI = 1.09-1.36); TB/HIV co-infection (aHR = 2.51, 95% CI = 2.26-2.79); facility-based direct observed therapy (DOT) option (aHR = 2.23, 95% CI = 1.95-2.72); having bacteriological unconfirmed TB results (aHR = 1.58, 95% CI = 1.42-1.76); and other referral type (aHR = 1.44, 95% CI = 1.16-1.78).

CONCLUSION

Advanced age, TB/HIV co-infection, bacteriological unconfirmed TB results, other referral types, receiving service at facility-based DOT option and obtaining service at the hospital level were significant contributors to TB death in Tanzania. Appropriate targeted intervention to improve TB referral systems, improve diagnostic capacity in the primary health facilities, minimize delay and misdiagnosis of TB patients might reduce TB mortality.

Impact of the diagnostic test Xpert MTB/RIF on patient outcomes for tuberculosis

BACKGROUND

The World Health Organization (WHO) recommends Xpert MTB/RIF in place of smear microscopy to diagnose tuberculosis (TB), and many countries have adopted it into their diagnostic algorithms. However, it is not clear whether the greater accuracy of the test translates into improved health outcomes.

OBJECTIVES

To assess the impact of Xpert MTB/RIF on patient outcomes in people being investigated for tuberculosis.

SEARCH METHODS

We searched the following databases, without language restriction, from 2007 to 24 July 2020: Cochrane Infectious Disease Group (CIDG) Specialized Register; CENTRAL; MEDLINE OVID; Embase OVID; CINAHL EBSCO; LILACS BIREME; Science Citation Index Expanded (Web of Science), Social Sciences citation index (Web of Science), and Conference Proceedings Citation Index - Social Science & Humanities (Web of Science). We also searched the WHO International Clinical Trials Registry Platform, ClinicalTrials.gov, and the Pan African Clinical Trials Registry for ongoing trials.

SELECTION CRITERIA

We included individual- and cluster-randomized trials, and before-after studies, in participants being investigated for tuberculosis. We analysed the randomized and non-randomized studies separately.  DATA COLLECTION AND ANALYSIS: For each study, two review authors independently extracted data, using a piloted data extraction tool. We assessed the risk of bias using Cochrane and Effective Practice and Organisation of Care (EPOC) tools. We used random effects meta-analysis to allow for heterogeneity between studies in setting and design.  The certainty of the  evidence in the randomized trials was assessed by GRADE.

MAIN RESULTS

We included 12 studies: eight were randomized controlled trials (RCTs), and four were before-and-after studies. Most included RCTs had a low risk of bias in most domains of the Cochrane 'Risk of bias' tool. There was inconclusive evidence of an effect of Xpert MTB/RIF on all-cause mortality, both overall (risk ratio (RR) 0.89, 95% confidence interval (CI) 0.75 to 1.05; 5 RCTs, 9932 participants, moderate-certainty evidence), and restricted to studies with six-month follow-up (RR 0.98, 95% CI 0.78 to 1.22; 3 RCTs, 8143 participants; moderate-certainty evidence). There was probably a reduction in mortality in participants known to be infected with HIV (odds ratio (OR) 0.80, 95% CI 0.67 to 0.96; 5 RCTs, 5855 participants; moderate-certainty evidence). It is uncertain whether Xpert MTB/RIF has no or a modest effect on the proportion of participants starting tuberculosis treatment who had a successful treatment outcome (OR) 1.10, 95% CI 0.96 to 1.26; 3RCTs, 4802 participants; moderate-certainty evidence). There was also inconclusive evidence of an effect on the  proportion of participants who were treated for tuberculosis (RR 1.10, 95% CI 0.98 to 1.23; 5 RCTs, 8793 participants; moderate-certainty evidence). The proportion of participants treated for tuberculosis who had bacteriological confirmation was probably higher in the Xpert MTB/RIF group (RR 1.44, 95% CI 1.29 to 1.61; 6 RCTs, 2068 participants; moderate-certainty evidence). The proportion of participants with bacteriological confirmation who were lost to follow-up pre-treatment was probably reduced (RR 0.59, 95% CI 0.41 to 0.85; 3 RCTs, 1217 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

We were unable to confidently rule in or rule out the effect on all-cause mortality of using Xpert MTB/RIF rather than smear microscopy. Xpert MTB/RIF probably reduces mortality among participants known to be infected with HIV. We are uncertain whether Xpert MTB/RIF has a modest effect or not on the proportion treated or, among those treated, on the proportion with a successful outcome. It probably does not have a substantial effect on these outcomes. Xpert MTB/RIF probably increases both the proportion of treated participants who had bacteriological confirmation, and the proportion with a laboratory-confirmed diagnosis who were treated. These findings may inform decisions about uptake alongside evidence on cost-effectiveness and implementation.

Comparing the impact of genotypic based diagnostic algorithm on time to treatment initiation and treatment outcomes among drug-resistant tuberculosis patients in Amhara region, Ethiopia

Background

To end Tuberculosis (TB) by 2030, early detection and timely treatment of Drug-Resistant Tuberculosis (DR-TB) is vital. The role of rapid, accurate, and sensitive DR-TB diagnostic tool is indispensable to accelerate the TB control program. There are evidence breaks in the time difference and its effect on treatment outcomes among different DR-TB diagnostic tools in Ethiopia. This article aimed to compare the different DR-TB diagnostic tools with time pointers and evaluate their effect on the treatment outcomes.

Method

We performed a retrospective chart review of 574 DR-TB patients from September 2010 to December 2017 to compare the impact of molecular DR-TB diagnostic tests (Xpert MTB/RIF, Line Probe Assay (LPA), and solid culture-based Drug Susceptibility Testing (DST)) on time to diagnosis, treatment initiation, and treatment Outcomes. Kruskual-Wallis test was employed to assess the presence of a significant difference in median time among the DR-TB diagnostic tests. Chi-Square and Fisher exact tests were used to test the presence of relations between treatment outcome and diagnostic tests.

Result

The data of 574 DR-TB patients were included in the analysis. From these, 321, 173, and 80 patients were diagnosed using Xpert MTB/RIF, Line Probe Assay (LPA), and solid culture-based DST, respectively. The median time in a day with (Interquartile range (IQR)) for Xpert MTB/RIF, LPA, and solid culture-based DST was from a first care-seeking visit to diagnosis: 2(0, 9), 4(1, 55), and 70(18, 182), from diagnosis to treatment initiation: 3(1, 8), 33(4, 76), and 44(9, 145), and from a first care-seeking visit to treatment initiation: 4(1, 11), 3(1, 12) and 76(3.75, 191) respectively. The shorter median time was observed in the Xpert MTB/RIF followed by the LPA, and this was statistically significant with a p-value <0.001. There was no statistically significant difference concerning treatment outcomes among the three DST tests.

Conclusion

Xpert MTB/RIF can mitigate the transmission of DR-TB significantly via quick diagnosis and treatment initiation followed by LPA as equating to the solid culture base DST, particularly in smear-positive patients. However, we didn’t see a statistically significant impact in terms of treatment outcomes. Xpert MTB/RIF can be used as the first test to diagnose DR-TB by further complimenting solid culture base DST to grasp the drug-resistance profile.

Comparison of small-sample standard-error corrections for generalised estimating equations in stepped wedge cluster randomised trials with a binary outcome: A simulation study

Generalised estimating equations with the sandwich standard-error estimator provide a promising method of analysis for stepped wedge cluster randomised trials. However, they have inflated type-one error when used with a small number of clusters, which is common for stepped wedge cluster randomised trials. We present a large simulation study of binary outcomes comparing bias-corrected standard errors from Fay and Graubard; Mancl and DeRouen; Kauermann and Carroll; Morel, Bokossa, and Neerchal; and Mackinnon and White with an independent and exchangeable working correlation matrix. We constructed 95% confidence intervals using a t-distribution with degrees of freedom including clusters minus parameters (DFC-P), cluster periods minus parameters, and estimators from Fay and Graubard (DFFG), and Pan and Wall. Fay and Graubard and an approximation to Kauermann and Carroll (with simpler matrix inversion) were unbiased in a wide range of scenarios with an independent working correlation matrix and more than 12 clusters. They gave confidence intervals with close to 95% coverage with DFFG with 12 or more clusters, and DFC-P with 18 or more clusters. Both standard errors were conservative with fewer clusters. With an exchangeable working correlation matrix, approximated Kauermann and Carroll and Fay and Graubard had a small degree of under-coverage.

Variation in the observed effect of Xpert MTB/RIF testing for tuberculosis on mortality: A systematic review and analysis of trial design considerations

Background: Most studies evaluating the effect of Xpert MTB/RIF testing for tuberculosis (TB) concluded that it did not reduce overall mortality compared to usual care. We conducted a systematic review to assess whether key study design and execution features contributed to earlier identification of patients with TB and decreased pre-treatment loss to follow-up, thereby reducing the potential impact of Xpert MTB/RIF testing. Methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, and Scopus for literature published from 1 st January 2009 to February 2019. We included all primary intervention studies that had evaluated the effect of Xpert MTB/RIF on mortality compared to usual care in participants with presumptive pulmonary TB. We critically reviewed features of included studies across: Study setting and context, Study population, Participant recruitment and enrolment, Study procedures, and Study follow-up. Results: We included seven randomised and one non-randomised study.  All included studies demonstrated relative reductions in overall mortality in the Xpert MTB/RIF arm ranging from 6% to 40%. However, mortality reduction was reported to be statistically significant in two studies. Study features that could explain the lack of observed effect on mortality included: the higher quality of care at study sites; inclusion of patients with a higher pre-test probability of TB leading to higher than expected empirical rates; performance of additional diagnostic testing not done in usual care leading to increased TB diagnosis or empiric treatment initiation; the recruitment of participants likely to return for follow-up; and involvement of study staff in ensuring adherence with care and follow-up. Conclusion: Most studies of Xpert MTB/RIF were designed and conducted in a manner that resulted in more patients being diagnosed and treated for TB, minimising the potential difference in mortality Xpert MTB/RIF testing could have achieved compared to usual care.

Cost-effectiveness analysis of Xpert in detecting Mycobacterium tuberculosis: A systematic review

OBJECTIVES

To report the cost-effectiveness of Xpert in detecting Mycobacterium tuberculosis (MTB) through a comprehensive systematic review.

METHODS

Specialized bibliographic databases were searched. Study quality was evaluated by commonly-used industry standards. Due to heterogeneity, evidences were synthesized narratively.

RESULTS

Four studies from intermediate-to-low tuberculosis (TB)-burdern areas and 17 studies from high-TB-burden areas were included. Smear microscopy, clinical diagnosis and chest radiography were mostly used for comparison. Cost elements varied considerably depending on the perspectives. Cost-effectiveness and cost-utility analyses were used by seven and fourteen studies, respectively. All studies were of high quality (CHEERS score of 78.4 and QHES score of 86.9). Average cost per test was 29.8 US$ for Xpert compared with 3.83 US$ for smear microscopy. Cost-effectiveness analyses mostly supported application of Xpert into areas under varying TB burdens.

CONCLUSIONS

Xpert seems cost-effective under respective willingness-to-pay thresholds in nations with differences in socioeconomy, HIV stress and geographical distribution. Nevertheless, policymakers will benefit from localized studies since regional economic/financial statuses and health-care system should also be considered apart from the reports of cost-effectiveness.

Novel methods for the analysis of stepped wedge cluster randomized trials

Stepped wedge cluster randomized trials (SW-CRTs) have become increasingly popular and are used for a variety of interventions and outcomes, often chosen for their feasibility advantages. SW-CRTs must account for time trends in the outcome because of the staggered rollout of the intervention. Robust inference procedures and nonparametric analysis methods have recently been proposed to handle such trends without requiring strong parametric modeling assumptions, but these are less powerful than model-based approaches. We propose several novel analysis methods that reduce reliance on modeling assumptions while preserving some of the increased power provided by the use of mixed effects models. In one method, we use the synthetic control approach to find the best matching clusters for a given intervention cluster. Another method makes use of within-cluster crossover information to construct an overall estimator. We also consider methods that combine these approaches to further improve power. We test these methods on simulated SW-CRTs, describing scenarios in which these methods have increased power compared with existing nonparametric methods while preserving nominal validity when mixed effects models are misspecified. We also demonstrate theoretical properties of these estimators with less restrictive assumptions than mixed effects models. Finally, we propose avenues for future research on the use of these methods; motivation for such research arises from their flexibility, which allows the identification of specific causal contrasts of interest, their robustness, and the potential for incorporating covariates to further increase power. Investigators conducting SW-CRTs might well consider such methods when common modeling assumptions may not hold.

Treatment outcomes, diagnostic and therapeutic impact: Xpert vs. smear. A systematic review and meta-analysis

BACKGROUND

Compared with smear microscopy, Xpert^® MTB/RIF has the potential to reduce delays in tuberculosis (TB) diagnosis and treatment initiation, and improve treatment outcomes. We reviewed publications comparing treatment outcomes of drug-susceptible TB patients diagnosed using Xpert vs. smear.

METHODS

Citations (2000-2016) reporting treatment outcomes of patients diagnosed using Xpert compared with smear were selected from PubMed, Scopus and conference abstracts. We conducted a systematic review and meta-analysis. Favorable (cured, completed) and unfavorable (failure, death, loss to follow-up) outcomes were pooled for meta-analysis; we also reviewed the number of TB cases diagnosed, time to treatment and empiric treatment. The Mantel-Haenszel method with a fixed-effect model was used; I² was calculated to measure heterogeneity.

RESULTS

From 13 citations, 43 594 TB patients were included and 4825 were with known TB treatment outcome. From the pooled analysis, an unfavorable outcomes among those diagnosed using Xpert compared with smear was 20.2%, 541/2675 vs. 21.9%, 470/2150 (risk ratio 0.92, 95%CI 0.82-1.02). Statistical heterogeneity was low (I² = 0.0%, P = 0.910). Compared with smear, Xpert was reported to be superior in increasing the number of TB patients diagnosed (2/9 citations), increasing bacteriologically confirmed TB (7/9 citations), reducing empiric treatment (3/5 citations), reducing time to diagnosis (2/3 citations), and reducing time to treatment initiation (1/5 citations).

CONCLUSIONS

Xpert implementation showed no discernible impact on treatment outcomes compared with conventional smear despite reduced time to diagnosis, time to treatment or reduced level of empiric treatment. Further research is required to learn more about gaps in the existing health system.

Tuberculosis treatment outcomes among people living with HIV diagnosed using Xpert MTB/RIF versus sputum-smear microscopy in Botswana: a stepped-wedge cluster randomised trial

Background

Xpert® MTB/RIF (Xpert) has high sensitivity for diagnosing tuberculosis (TB) compared to sputum-smear microscopy (smear) and can reduce time-to-diagnosis, time-to-treatment and potentially unfavorable patient-level treatment outcome.

Methods

People living with HIV (PLHIV) initiating antiretroviral therapy at 22 HIV clinics were enrolled and underwent systematic screening for TB (August 2012–November 2014). GeneXpert instruments were deployed following a stepped-wedge design at 13 centers from October 2012–June 2013. Treatment outcomes classified as an unfavorable outcome (died, treatment failure or loss-to-follow-up) or favorable outcome (cured and treatment completed). To determine outcome, smear was performed at month 5 or 6. Empiric treatment was defined as initiating treatment without/before receiving TB-positive results. Adjusting for intra-facility correlation, we compared patient-level treatment outcomes between patients screened using smear (smear arm)- and Xpert-based algorithms (Xpert arm).

Results

Among 6041 patients enrolled (smear arm, 1816; Xpert arm, 4225), 256 (199 per 2985 and 57 per 1582 person-years of follow-up in Xpert and smear arms, respectively; adjusted incidence rate ratio, 9.07; 95% confidence interval [CI]: 4.70–17.48; p < 0.001) received TB diagnosis and were treated. TB treatment outcomes were available for 203 patients (79.3%; Xpert, 157; smear, 46). Unfavorable outcomes were reported for 21.7% (10/46) in the smear and 13.4% (21/157) in Xpert arm (adjusted hazard ratio, 1.40; 95% CI: 0.75–2.26; p = 0.268). Compared to smear, in Xpert arm median days from sputum collection to TB treatment was 6 days (interquartile range [IQR] 2–17 versus 22 days [IQR] 3–51), p = 0.005; patients with available sputum test result had microbiologically confirmed TB in 59.0% (102/173) versus 41.9% (18/43), adjusted Odds Ratio [aOR], 2.00, 95% CI: 1.01–3.96, p = 0.048). In smear arm empiric treatment was 68.4% (39/57) versus 48.7% (97/199), aOR, 2.28, 95% CI: 1.24–4.20, p = 0.011), compared to Xpert arm.

Conclusions

TB treatment outcomes were similar between the smear and Xpert arms. However, compared to the smear arm, more patients in the Xpert arm received a TB diagnosis, had a microbiologically confirmed TB, and had a shorter time-to-treatment, and had a lower empiric treatment. Further research is recommended to identify potential gaps in the Botswana health system and similar settings.

Trial registration

ClinicalTrials.gov Identifier: NCT02538952. Retrospectively registered on 2 September 2015.

swpermute: Permutation tests for Stepped-Wedge Cluster-Randomised Trials

Permutation tests are useful in stepped-wedge trials to provide robust statistical tests of intervention-effect estimates. However, the Stata command permute does not produce valid tests in this setting because individual observations are not exchangeable. We introduce the swpermute command that permutes clusters to sequences to maintain exchangeability. The command provides additional functionality to aid users in performing analyses of stepped-wedge trials. In particular, we include the option "withinperiod" that performs the specified analysis separately in each period of the study with the resulting period-specific intervention-effect estimates combined as a weighted average. We also include functionality to test non-zero null hypotheses to aid the construction of confidence intervals. Examples of the application of swpermute are given using data from a trial testing the impact of a new tuberculosis diagnostic test on bacterial confirmation of a tuberculosis diagnosis.

Variation in the observed effect of Xpert MTB/RIF testing for tuberculosis on mortality: A systematic review and analysis of trial design considerations

Background: Most studies evaluating the effect of Xpert MTB/RIF testing for tuberculosis (TB) concluded that it did not reduce overall mortality compared to usual care. We conducted a systematic review to assess whether key study design and execution features contributed to earlier identification of patients with TB and decreased pre-treatment loss to follow-up, thereby reducing the potential impact of Xpert MTB/RIF testing. Methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, and Scopus for literature published from 1 st January 2009 to February 2019. We included all primary intervention studies that had evaluated the effect of Xpert MTB/RIF on mortality compared to usual care in participants with presumptive pulmonary TB. We critically reviewed features of included studies across: Study setting and context, Study population, Participant recruitment and enrolment, Study procedures, and Study follow-up. Results: We included seven randomised and one non-randomised study.  All included studies demonstrated relative reductions in overall mortality in the Xpert MTB/RIF arm ranging from 6% to 40%. However, mortality reduction was reported to be statistically significant in two studies. Study features that could explain the lack of observed effect on mortality included: the higher quality of care at study sites; inclusion of patients with a higher pre-test probability of TB leading to higher than expected empirical rates; performance of additional diagnostic testing not done in usual care leading to increased TB diagnosis or empiric treatment initiation; the recruitment of participants likely to return for follow-up; and involvement of study staff in ensuring adherence with care and follow-up. Conclusion: Most studies of Xpert MTB/RIF were designed and conducted in a manner that resulted in more patients being diagnosed and treated for TB, minimising the potential difference in mortality Xpert MTB/RIF testing could have achieved compared to usual care.

The effect of sputum quality and volume on the yield of bacteriologically-confirmed TB by Xpert MTB/RIF and smear

Introduction

The World Health Organization endorsed (2010) the use of Xpert MTB/RIF and countries are shifting from smear microscopy (smear)-based to Xpert MTB/RIF-based tuberculosis (TB) diagnostic algorithms. As with smear, sputum quality may predict the likelihood of obtaining a bacteriologically-confirmed TB when using Xpert MTB/RIF.

Methods

From 08/12-11/2014, all people living with HIV were recruited at 22 clinics. For patients screened positive using the four TB symptoms their sputa were tested by Xpert MTB/RIF and smear. Laboratorians assessed and recorded sputum appearance and volume. The yield of bacteriologically-positive sputum evaluated using Xpert MTB/RIF and smear, likelihood-ratios were calculated.

Results

Among 6,041 patients enrolled 2,296 were presumptive TB, 1,305 (56.8%) had > 1 sputa collected and 644/1,305 (49.3%) had both Xpert MTB/RIF and smear results. Since >1 sputa collected from 644 patients 954 sputa were tested by Xpert MTB/RIF and smear. Bacteriologically-positive sputum was two-fold higher with Xpert MTB/RIF 11.4% versus smear 5.3%, p < 0.001. Sputum appearance and quantity were not predictive of bacteriologically-positive results, except volume of 2ml to < 3ml, tested by Xpert MTB/RIF LR+= 1.26 (95% CI, 1.05–1.50).

Conclusion

Xpert MTB/RIF test yield to bacteriologically-positive sputum was superior to smear. Sputum quality and quantity, however, were not consistently predictive of bacteriologically-positive results by Xpert MTB/RIF or smear.

Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults

BACKGROUND

Xpert MTB/RIF (Xpert MTB/RIF) and Xpert MTB/RIF Ultra (Xpert Ultra), the newest version, are the only World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in persons with signs and symptoms of tuberculosis, at lower health system levels. A previous Cochrane Review found Xpert MTB/RIF sensitive and specific for tuberculosis (Steingart 2014). Since the previous review, new studies have been published. We performed a review update for an upcoming WHO policy review.

OBJECTIVES

To determine diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for tuberculosis in adults with presumptive pulmonary tuberculosis (PTB) and for rifampicin resistance in adults with presumptive rifampicin-resistant tuberculosis.

SEARCH METHODS

We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, to 11 October 2018, without language restriction.

SELECTION CRITERIA

Randomized trials, cross-sectional, and cohort studies using respiratory specimens that evaluated Xpert MTB/RIF, Xpert Ultra, or both against the reference standard, culture for tuberculosis and culture-based drug susceptibility testing or MTBDRplus for rifampicin resistance.

DATA COLLECTION AND ANALYSIS

Four review authors independently extracted data using a standardized form. When possible, we also extracted data by smear and HIV status. We assessed study quality using QUADAS-2 and performed meta-analyses to estimate pooled sensitivity and specificity separately for tuberculosis and rifampicin resistance. We investigated potential sources of heterogeneity. Most analyses used a bivariate random-effects model. For tuberculosis detection, we first estimated accuracy using all included studies and then only the subset of studies where participants were unselected, i.e. not selected based on prior microscopy testing.

MAIN RESULTS

We identified in total 95 studies (77 new studies since the previous review): 86 studies (42,091 participants) evaluated Xpert MTB/RIF for tuberculosis and 57 studies (8287 participants) for rifampicin resistance. One study compared Xpert MTB/RIF and Xpert Ultra on the same participant specimen.Tuberculosis detectionOf the total 86 studies, 45 took place in high tuberculosis burden and 50 in high TB/HIV burden countries. Most studies had low risk of bias.Xpert MTB/RIF pooled sensitivity and specificity (95% credible Interval (CrI)) were 85% (82% to 88%) and 98% (97% to 98%), (70 studies, 37,237 unselected participants; high-certainty evidence). We found similar accuracy when we included all studies.For a population of 1000 people where 100 have tuberculosis on culture, 103 would be Xpert MTB/RIF-positive and 18 (17%) would not have tuberculosis (false-positives); 897 would be Xpert MTB/RIF-negative and 15 (2%) would have tuberculosis (false-negatives).Xpert Ultra sensitivity (95% confidence interval (CI)) was 88% (85% to 91%) versus Xpert MTB/RIF 83% (79% to 86%); Xpert Ultra specificity was 96% (94% to 97%) versus Xpert MTB/RIF 98% (97% to 99%), (1 study, 1439 participants; moderate-certainty evidence).Xpert MTB/RIF pooled sensitivity was 98% (97% to 98%) in smear-positive and 67% (62% to 72%) in smear-negative, culture-positive participants, (45 studies). Xpert MTB/RIF pooled sensitivity was 88% (83% to 92%) in HIV-negative and 81% (75% to 86%) in HIV-positive participants; specificities were similar 98% (97% to 99%), (14 studies).Rifampicin resistance detectionXpert MTB/RIF pooled sensitivity and specificity (95% Crl) were 96% (94% to 97%) and 98% (98% to 99%), (48 studies, 8020 participants; high-certainty evidence).For a population of 1000 people where 100 have rifampicin-resistant tuberculosis, 114 would be positive for rifampicin-resistant tuberculosis and 18 (16%) would not have rifampicin resistance (false-positives); 886 would be would be negative for rifampicin-resistant tuberculosis and four (0.4%) would have rifampicin resistance (false-negatives).Xpert Ultra sensitivity (95% CI) was 95% (90% to 98%) versus Xpert MTB/RIF 95% (91% to 98%); Xpert Ultra specificity was 98% (97% to 99%) versus Xpert MTB/RIF 98% (96% to 99%), (1 study, 551 participants; moderate-certainty evidence).

AUTHORS' CONCLUSIONS

We found Xpert MTB/RIF to be sensitive and specific for diagnosing PTB and rifampicin resistance, consistent with findings reported previously. Xpert MTB/RIF was more sensitive for tuberculosis in smear-positive than smear-negative participants and HIV-negative than HIV-positive participants. Compared with Xpert MTB/RIF, Xpert Ultra had higher sensitivity and lower specificity for tuberculosis and similar sensitivity and specificity for rifampicin resistance (1 study). Xpert MTB/RIF and Xpert Ultra provide accurate results and can allow rapid initiation of treatment for multidrug-resistant tuberculosis.

Gridlock from diagnosis to treatment of multidrug-resistant tuberculosis in Tanzania: low accessibility of molecular diagnostic services and lack of healthcare worker empowerment in 28 districts of 5 high burden TB regions with mixed methods evaluation

BACKGROUND

Multidrug-resistant tuberculosis (MDR-TB) outcomes are adversely impacted by delay in diagnosis and treatment.

METHODS

Mixed qualitative and quantitative approaches were utilized to identify healthcare system related barriers to implementation of molecular diagnostics for MDR-TB. Randomly sampled districts from the 5 highest TB burden regions were enrolled during the 4th quarter of 2016. District TB & Leprosy Coordinators (DTLCs), and District AIDS Coordinators (DACs) were interviewed, along with staff from all laboratories within the selected districts where molecular diagnostics tests for MDR-TB were performed. Furthermore, the 2015 registers were audited for all drug-susceptible but retreatment TB cases and TB collaborative practices in HIV clinics, as these patients were in principal targeted for drug susceptibility testing by rapid molecular diagnostics.

RESULTS

Twenty-eight TB districts from the 5 regions had 399 patients reviewed for retreatment with a drug-susceptible regimen. Only 160 (40%) had specimens collected for drug-susceptibility testing, and of those specimens only 120 (75%) had results communicated back to the clinic. MDR-TB was diagnosed in 16 (13.3%) of the 120 specimens but only 12 total patients were ultimately referred for treatment. Furthermore, among the HIV/AIDS clinics served in 2015, the median number of clients with TB diagnosis was 92 cases [IQR 32-157] yet only 2 people living with HIV were diagnosed with MDR-TB throughout the surveyed districts. Furthermore, the districts generated 53 front-line healthcare workers for interviews. DTLCs with intermediate or no knowledge on the clinical application of XpertMTB/RIF were 3 (11%), and 10 (39%), and DACs with intermediate or no knowledge were 0 (0%) and 2 (8%) respectively (p = 0.02). Additionally, 11 (100%) of the laboratories surveyed had only the 4-module XpertMTB/RIF equipment. The median time that XpertMTB/RIF was not functional in the 12 months prior to the investigation was 2 months (IQR 1-4).

CONCLUSIONS

Underutilization of molecular diagnostics in high-risk groups was a function of a lack of front-line healthcare workforce empowerment and training, and a lack of equipment access, which likely contributed to the observed delay in MDR-TB diagnosis in Tanzania.

Effect of Xpert MTB/RIF on clinical outcomes in routine care settings: individual patient data meta-analysis

BACKGROUND

Xpert MTB/RIF, the most widely used automated nucleic acid amplification test for tuberculosis, is available in more than 130 countries. Although diagnostic accuracy is well documented, anticipated improvements in patient outcomes have not been clearly identified. We performed an individual patient data meta-analysis to examine improvements in patient outcomes associated with Xpert MTB/RIF.

METHODS

We searched PubMed, Embase, ClinicalTrials.gov, and the Pan African Clinical Trials Registry from inception to Feb 1, 2018, for randomised controlled trials (RCTs) comparing the use of Xpert MTB/RIF with sputum smear microscopy as tests for tuberculosis diagnosis in adults (aged 18 years or older). We excluded studies of patients with extrapulmonary tuberculosis, and studies in which mortality was not assessed. We used a two-stage approach for our primary analysis and a one-stage approach for the sensitivity analysis. To assess the primary outcome of cumulative 6-month all-cause mortality, we first performed logistic regression models (random effects for cluster randomised trials, with robust SEs for multicentre studies) for each trial, and then pooled the odds ratio (OR) estimates by a fixed-effects (inverse variance) or random-effects (Der Simonian Laird) meta-analysis. We adjusted for age and gender, and stratified by HIV status and previous tuberculosis-treatment history. The study protocol has been registered with PROSPERO, number CRD42014013394.

FINDINGS

Our search identified 387 studies, of which five RCTs were eligible for analysis. 8567 adult clinic attendees (4490 [63·5%] of 7074 participants for whom data were available were HIV-positive) were tested for tuberculosis with Xpert MTB/RIF (Xpert group) versus sputum smear microscopy (sputum smear group), across five low-income and middle-income countries (South Africa, Brazil, Zimbabwe, Zambia, and Tanzania). The primary outcome (reported in three studies) occurred in 182 (4·5%) of 4050 patients in the Xpert group and 217 (5·3%) of 4093 patients in the smear group (pooled adjusted OR 0·88, 95% CI 0·68-1·14 [p=0·34]; for HIV-positive individuals OR 0·83, 0·65-1·05 [p=0·12]). Kaplan-Meier estimates showed a lower rate of death (12·73 per 100 person-years in the Xpert group vs 16·38 per 100 person-years in the sputum smear group) for HIV-positive patients (hazard ratio 0·76, 95% CI 0·60-0·97; p=0·03). The risk of bias was assessed as reasonable and the statistical heterogeneity across studies was low (I²<20% for the primary outcome).

INTERPRETATION

Despite individual patient data analysis from five RCTs, we were unable to confidently rule in nor rule out an Xpert MTB/RIF-associated reduction in mortality among outpatients tested for tuberculosis. Reduction in mortality among HIV-positive patients in a secondary analysis suggests the possibility of population-level impact.

FUNDING

US National Institutes of Health.

Systematic review showed that stepped-wedge cluster randomized trials often did not reach their planned sample size

OBJECTIVE

To determine how often stepped-wedge cluster randomized controlled trials reach their planned sample size, and what reasons are reported for choosing a stepped-wedge trial design.

STUDY DESIGN AND SETTING

We conducted a PubMed literature search (period 2012 to 2017) and included articles describing the results of a stepped-wedge cluster randomized trial. We calculated the percentage of studies reaching their prespecified number of participants and clusters, and we summarized the reasons for choosing the stepped-wedge trial design as well as difficulties during enrollment.

RESULTS

Forty-six individual stepped-wedge studies from a total of 53 articles were included in our review. Of the 35 studies, for which recruitment rate could be calculated, 69% recruited their planned number of participants, with 80% having recruited the planned number of clusters. Ethical reasons were the most common motivation for choosing the stepped-wedge trial design. Most important difficulties during study conduct were dropout of clusters and delayed implementation of the intervention.

CONCLUSION

About half of recently published stepped-wedge trials reached their planned sample size indicating that recruitment is also a major problem in these trials. Still, the stepped-wedge trial design can yield practical, ethical, and methodological advantages.

Cost-effectiveness of GeneXpert and LED-FM for diagnosis of pulmonary tuberculosis: A systematic review

BACKGROUND

Early and accurate diagnosis of tuberculosis is a priority for TB programs globally to initiate treatment early and improve treatment outcomes. Currently, Ziehl-Neelsen (ZN) stain-based microscopy, GeneXpert and Light Emitting Diode-Fluorescence Microscopy (LED-FM) are used for diagnosing pulmonary drug sensitive tuberculosis. Published evidence synthesising the cost-effectiveness of these diagnostic tools is scarce.

METHODOLOGY

PubMed, EMBASE and Cost-effectiveness analysis registry were searched for studies that reported on the cost-effectiveness of GeneXpert and LED-FM, compared to ZN microscopy for diagnosing pulmonary TB. Risk of bias was assessed independently by four authors using the Consensus Health Economic Criteria (CHEC) extended checklist. The data variables included the study settings, population, type of intervention, type of comparator, year of study, duration of study, type of study design, costs for the test and the comparator and effectiveness indicators. Incremental cost-effectiveness ratio (ICER) was used for assessing the relative cost-effectiveness in this review.

RESULTS

Of the 496 studies identified by the search, thirteen studies were included after removing duplicates and studies that did not fulfil inclusion criteria. Four studies compared LED-FM with ZN and nine studies compared GeneXpert with ZN. Three studies used patient cohorts and eight were modelling studies with hypothetical cohorts used to evaluate cost-effectiveness. All these studies were conducted from a health system perspective, with four studies utilising cost utility analysis. There were considerable variations in costing parameters and effectiveness indicators that precluded meta-analysis. The key findings from the included studies suggest that LED-FM and GeneXpert may be cost effective for pulmonary TB diagnosis from a health system perspective.

CONCLUSION

Our review identifies a consistent trend of the cost effectiveness of LED-FM and GeneXpert for pulmonary TB diagnosis in different countries with diverse context of socio-economic condition, HIV burden and geographical distribution. However, all the studies used different parameters to estimate the impact of these tools and this underscores the need for improving the methodological issues related to the conduct and reporting of cost-effectiveness studies.

A scoping review on the field validation and implementation of rapid diagnostic tests for vector-borne and other infectious diseases of poverty in urban areas

BACKGROUND

Health personnel face challenges in diagnosing vector-borne and other diseases of poverty in urban settings. There is a need to know what rapid diagnostic technologies are available, have been properly assessed, and are being implemented to improve control of these diseases in the urban context. This paper characterizes evidence on the field validation and implementation in urban areas of rapid diagnostics for vector-borne diseases and other diseases of poverty.

MAIN BODY

A scoping review was conducted. Peer-reviewed and grey literature were searched using terms describing the targeted infectious diseases, diagnostics evaluations, rapid tests, and urban setting. The review was limited to studies published between 2000 and 2016 in English, Spanish, French, and Portuguese. Inclusion and exclusion criteria were refined post hoc to identify relevant literature regardless of study design and geography. A total of 179 documents of the 7806 initially screened were included in the analysis. Malaria (n = 100) and tuberculosis (n = 47) accounted for the majority of studies that reported diagnostics performance, impact, and implementation outcomes. Fewer studies, assessing mainly performance, were identified for visceral leishmaniasis (n = 9), filariasis and leptospirosis (each n = 5), enteric fever and schistosomiasis (each n = 3), dengue and leprosy (each n = 2), and Chagas disease, human African trypanosomiasis, and cholera (each n = 1). Reported sensitivity of rapid tests was variable depending on several factors. Overall, specificities were high (> 80%), except for schistosomiasis and cholera. Impact and implementation outcomes, mainly acceptability and cost, followed by adoption, feasibility, and sustainability of rapid tests are being evaluated in the field. Challenges to implementing rapid tests range from cultural to technical and administrative issues.

CONCLUSIONS

Rapid diagnostic tests for vector-borne and other diseases of poverty are being used in the urban context with demonstrated impact on case detection. However, most evidence comes from malaria rapid diagnostics, with variable results. While rapid tests for tuberculosis and visceral leishmaniasis require further implementation studies, more evidence on performance of current tests or development of new alternatives is needed for dengue, Chagas disease, filariasis, leptospirosis, enteric fever, human African trypanosomiasis, schistosomiasis and cholera.

Tuberculosis: renewed challenge in Brazil

This article reviews tuberculosis control actions performed over the last decade, at a global level. The perspectives for the fulfillment of the goals of the new Global Tuberculosis Elimination Plan are described, where the insertion of social protection (Pillar 2) and research (Pillar 3) will play an innovative and strategic role, especially in high-burden countries, like Brazil.

Robust analysis of stepped wedge trials using cluster-level summaries within periods

In stepped‐wedge trials (SWTs), the intervention is rolled out in a random order over more than 1 time‐period. SWTs are often analysed using mixed‐effects models that require strong assumptions and may be inappropriate when the number of clusters is small.

We propose a non‐parametric within‐period method to analyse SWTs. This method estimates the intervention effect by comparing intervention and control conditions in a given period using cluster‐level data corresponding to exposure. The within‐period intervention effects are combined with an inverse‐variance‐weighted average, and permutation tests are used. We present an example and, using simulated data, compared the method to (1) a parametric cluster‐level within‐period method, (2) the most commonly used mixed‐effects model, and (3) a more flexible mixed‐effects model. We simulated scenarios where period effects were common to all clusters, and when they varied according to a distribution informed by routinely collected health data.

The non‐parametric within‐period method provided unbiased intervention effect estimates with correct confidence‐interval coverage for all scenarios. The parametric within‐period method produced confidence intervals with low coverage for most scenarios. The mixed‐effects models' confidence intervals had low coverage when period effects varied between clusters but had greater power than the non‐parametric within‐period method when period effects were common to all clusters.

The non‐parametric within‐period method is a robust method for analysing SWT. The method could be used by trial statisticians who want to emphasise that the SWT is a randomised trial, in the common position of being uncertain about whether data will meet the assumptions necessary for mixed‐effect models.

Unsuccessful Xpert® MTB/RIF results: the Nigerian experience

Setting: Nigeria, a high tuberculosis (TB) burden country. Objective: To study the rate, distribution and causes of unsuccessful Xpert^® MTB/RIF test outcomes, with the aim of identifying key areas that need to be strengthened for optimal performance of the assay. Design: This was a retrospective analysis of data uploaded between January and December 2015 from Xpert facilities to the central server using GXAlert. Result: Of 52 219 test results uploaded from 176 Xpert machines, 22.5% were positive for Mycobacterium tuberculosis, 10.8% of which were rifampicin-resistant; 4.7% of the total number of results were invalid, 4.2% had error results and 2.1% no result outcomes. Technical errors were most frequent (69%); these were non-seasonal and occurred in all geopolitical regions and at all health facility levels. Temperature-related errors were more prevalent in the North-West Region, with peaks in April to June. Peak periods for temperature and machine malfunction errors coincided with the periods of low utilisation of the assay. Conclusion: The key challenge affecting performance was poor adherence to standard operating procedures. Periodic refresher training courses, regular supervision, preventive maintenance of Xpert machines and proper storage of cartridges are strategies that could improve Xpert performance.

Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential?

BACKGROUND

Nearly two decades after completion of the genome sequence of Mycobacterium tuberculosis (MTB), and with the advent of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been applied to a wide range of clinical scenarios. Starting in 2017, England is the first country in the world to pioneer its use on a national scale for the diagnosis of tuberculosis, detection of drug resistance, and typing of MTB.

AIMS

This narrative review critically analyses the current applications of WGS for MTB and explains how close we are to realizing its full potential as a diagnostic, epidemiologic, and research tool.

SOURCES

We searched for reports (both original articles and reviews) published in English up to 31 May 2017, with combinations of the following keywords: whole-genome sequencing, Mycobacterium, and tuberculosis. MEDLINE, Embase, and Scopus were used as search engines. We included articles that covered different aspects of whole-genome sequencing in relation to MTB.

CONTENT

This review focuses on three main themes: the role of WGS for the prediction of drug susceptibility, MTB outbreak investigation and genetic diversity, and research applications of NGS.

IMPLICATIONS

Many of the original expectations have been accomplished, and we believe that with its unprecedented sensitivity and power, WGS has the potential to address many unanswered questions in the near future. However, caution is still needed when interpreting WGS data as there are some important limitations to be aware of, from correct interpretation of drug susceptibilities to the bioinformatic support needed.

[Budget impact of the incorporation of GeneXpert MTB/RIF for diagnosis of pulmonary tuberculosis from the perspective of the Brazilian Unified National Health System, Brazil, 2013-2017]

The study aimed to estimate the budget impact of GeneXpert MTB/RIF for diagnosis of tuberculosis from the perspective of the Brazilian National Program for Tuberculosis Control, drawing on a static model using the epidemiological method, from 2013 to 2017. GeneXpert MTB/RIF was compared with two diagnostic sputum smear tests. The study used epidemiological, population, and cost data, exchange rates, and databases from the Brazilian Unified National Health System. Sensitivity analysis of scenarios was performed. Incorporation of GeneXpert MTB/RIF would cost BRL 147 million (roughly USD 45 million) in five years and would have an impact of 23 to 26% in the first two years and some 11% between 2015 and 2017. The results can support Brazilian and other Latin American health administrators in planning and managing the decision on incorporating the technology.

Cost-effectiveness of Xpert MTB/RIF for tuberculosis diagnosis in South Africa: a real-world cost analysis and economic evaluation

BACKGROUND

In 2010 a new diagnostic test for tuberculosis, Xpert MTB/RIF, received a conditional programmatic recommendation from WHO. Several model-based economic evaluations predicted that Xpert would be cost-effective across sub-Saharan Africa. We investigated the cost-effectiveness of Xpert in the real world during national roll-out in South Africa.

METHODS

For this real-world cost analysis and economic evaluation, we applied extensive primary cost and patient event data from the XTEND study, a pragmatic trial examining Xpert introduction for people investigated for tuberculosis in 40 primary health facilities (20 clusters) in South Africa enrolled between June 8, and Nov 16, 2012, to estimate the costs and cost per disability-adjusted life-year averted of introducing Xpert as the initial diagnostic test for tuberculosis, compared with sputum smear microscopy (the standard of care).

FINDINGS

The mean total cost per study participant for tuberculosis investigation and treatment was US$312·58 (95% CI 252·46-372·70) in the Xpert group and $298·58 (246·35-350·82) in the microscopy group. The mean health service (provider) cost per study participant was $168·79 (149·16-188·42) for the Xpert group and $160·46 (143·24-177·68) for the microscopy group of the study. Considering uncertainty in both cost and effect using a wide range of willingness to pay thresholds, we found less than 3% probability that Xpert introduction improved the cost-effectiveness of tuberculosis diagnostics.

INTERPRETATION

After analysing extensive primary data collection during roll-out, we found that Xpert introduction in South Africa was cost-neutral, but found no evidence that Xpert improved the cost-effectiveness of tuberculosis diagnosis. Our study highlights the importance of considering implementation constraints, when predicting and evaluating the cost-effectiveness of new tuberculosis diagnostics in South Africa.

FUNDING

Bill & Melinda Gates Foundation.

Impact of the GeneXpert MTB/RIF Technology on Tuberculosis Control

Molecular technology revolutionized the diagnosis of tuberculosis (TB) with a paradigm shift to faster, more sensitive, clinically relevant patient care. The most recent molecular leader is the GeneXpert MTB/RIF assay (Xpert) (Cepheid, Sunnyvale, CA), which was endorsed by the World Health Organization with unprecedented speed in December 2010 as the initial diagnostic for detection of HIV-associated TB and for where high rates of drug resistance are suspected. South Africa elected to take an aggressive smear replacement approach to facilitate earlier diagnosis and treatment through the decision to implement the Xpert assay nationally in March 2011, against the backdrop of approximately 6.3 million HIV-infected individuals, one of highest global TB and HIV coinfection rates, no available implementation models, uncertainties around field performance and program costs, and lack of guidance on how to operationalize the assay into existing complex clinical algorithms. South Africa's national implementation was conducted as a phased, forecasted, and managed approach (March 2011 to September 2013), through political will and both treasury-funded and donor-funded support. Today there are 314 GeneXperts across 207 microscopy centers; over 8 million assays have been conducted, and South Africa accounts for over half the global test cartridge usage. As with any implementation of new technology, challenges were encountered, both predicted and unexpected. This chapter discusses the challenges and consequences of such large-scale implementation efforts, the opportunities for new innovations, and the need to strengthen health systems, as well as the impact of the Xpert assay on rifampin-sensitive and multidrug-resistant TB patient care that translated into global TB control as we move toward the sustainable development goals.

Xpert MTB/RIF - why the lack of morbidity and mortality impact in intervention trials?

Compared with smear microscopy, the Xpert MTB/RIF assay (Xpert), with superior accuracy and capacity to diagnose rifampicin resistance, has advanced TB diagnostic capability. However, recent trials of Xpert impact have not demonstrated reductions in patient morbidity and mortality. We conducted a narrative review of Xpert impact trials to summarize which patient-relevant outcomes Xpert has improved and explore reasons for no observed morbidity or mortality reductions. We searched PubMed, Google Scholar, Cochrane Library and Embase and identified eight trials meeting inclusion criteria: three individually randomized, three cluster-randomized, and two pre-post trials. In six trials Xpert increased diagnostic yield of bacteriologically-confirmed TB from sputa and in four trials Xpert shortened time to TB treatment. However, all-cause mortality was similar between arms in all six trials reporting this outcome, and the only trial to assess Xpert impact on morbidity reported no impact. Trial characteristics that might explain lack of observed impact on morbidity and mortality include: higher rates of empiric TB treatment in microscopy compared with Xpert arms, enrollment of study populations not comprised exclusively of populations most likely to benefit from Xpert, and health system weaknesses. So far as equipoise exists, future trials that address past limitations are needed to inform Xpert use in resource-limited settings.

Development, roll-out and impact of Xpert MTB/RIF for tuberculosis: what lessons have we learnt and how can we do better?

The global roll-out of Xpert MTB/RIF (Cepheid Inc., Sunnyvale, CA, USA) has changed the diagnostic landscape of tuberculosis (TB). More than 16 million tests have been performed in 122 countries since 2011, and detection of multidrug-resistant TB has increased three- to eight-fold compared to conventional testing. The roll-out has galvanised stakeholders, from donors to civil society, and paved the way for universal drug susceptibility testing. It has attracted new product developers to TB, resulting in a robust molecular diagnostics pipeline. However, the roll-out has also highlighted gaps that have constrained scale-up and limited impact on patient outcomes. The roll-out has been hampered by high costs for under-funded programmes, unavailability of a complete solution package (notably comprehensive training, quality assurance, implementation plans, inadequate service and maintenance support) and lack of impact assessment. Insufficient focus has been afforded to effective linkage to care of diagnosed patients, and clinical impact has been blunted by weak health systems. In many countries the private sector plays a dominant role in TB control, yet this sector has limited access to subsidised pricing. In light of these lessons, we advocate for a comprehensive diagnostics implementation approach, including increased engagement of in-country stakeholders for product launch and roll-out, broader systems strengthening in preparation for new technologies, as well as quality impact data from programmatic settings.

A comprehensive diagnostic solution approach including systems strengthening is essential for TB diagnostics impacthttp://ow.ly/uWSy300CfJT

Stepped wedge cluster randomised trials: a review of the statistical methodology used and available

BACKGROUND

Previous reviews have focussed on the rationale for employing the stepped wedge design (SWD), the areas of research to which the design has been applied and the general characteristics of the design. However these did not focus on the statistical methods nor addressed the appropriateness of sample size methods used.This was a review of the literature of the statistical methodology used in stepped wedge cluster randomised trials.

METHODS

Literature Review. The Medline, Embase, PsycINFO, CINAHL and Cochrane databases were searched for methodological guides and RCTs which employed the stepped wedge design.

RESULTS

This review identified 102 trials which employed the stepped wedge design compared to 37 from the most recent review by Beard et al. 2015. Forty six trials were cohort designs and 45 % (n = 46) had fewer than 10 clusters. Of the 42 articles discussing the design methodology 10 covered analysis and seven covered sample size. For cohort stepped wedge designs there was only one paper considering analysis and one considering sample size methods. Most trials employed either a GEE or mixed model approach to analysis (n = 77) but only 22 trials (22 %) estimated sample size in a way which accounted for the stepped wedge design that was subsequently used.

CONCLUSIONS

Many studies which employ the stepped wedge design have few clusters but use methods of analysis which may require more clusters for unbiased and efficient intervention effect estimates. There is the need for research on the minimum number of clusters required for both types of stepped wedge design. Researchers should distinguish in the sample size calculation between cohort and cross sectional stepped wedge designs. Further research is needed on the effect of adjusting for the potential confounding of time on the study power.

Programmatic Management of Drug-Resistant Tuberculosis: An Updated Research Agenda

Introduction

There are numerous challenges in delivering appropriate treatment for multidrug-resistant tuberculosis (MDR-TB) and the evidence base to guide those practices remains limited. We present the third updated Research Agenda for the programmatic management of drug-resistant TB (PMDT), assembled through a literature review and survey.

Methods

Publications citing the 2008 research agenda and normative documents were reviewed for evidence gaps. Gaps were formulated into questions and grouped as in the 2008 research agenda: Laboratory Support, Treatment Strategy, Programmatically Relevant Research, Epidemiology, and Management of Contacts. A survey was distributed through snowball sampling to identify research priorities. Respondent priority rankings were scored and summarized by mean. Sensitivity analyses explored weighting and handling of missing rankings.

Results

Thirty normative documents and publications were reviewed for stated research needs; these were collapsed into 56 research questions across 5 categories. Of more than 500 survey recipients, 133 ranked priorities within at least one category. Priorities within categories included new diagnostics and their effect on improving treatment outcomes, improved diagnosis of paucibacillary and extra pulmonary TB, and development of shorter, effective regimens. Interruption of nosocomial transmission and treatment for latent TB infection in contacts of known MDR−TB patients were also top priorities in their respective categories. Results were internally consistent and robust.

Discussion

Priorities retained from the 2008 research agenda include shorter MDR-TB regimens and averting transmission. Limitations of recent advances were implied in the continued quest for: shorter regimens containing new drugs, rapid diagnostics that improve treatment outcomes, and improved methods of estimating burden without representative data.

Conclusion

There is continuity around the priorities for research in PMDT. Coordinated efforts to address questions regarding shorter treatment regimens, knowledge of disease burden without representative data, and treatment for LTBI in contacts of known DR-TB patients are essential to stem the epidemic of TB, including DR-TB.